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Cryptic Diversity of Japanese Diaphanosoma (Crustacea: Cladocera)

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Cryptic Diversity of Japanese Diaphanosoma (Crustacea: Cladocera) View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by FBA Journal System (Freshwater Biological Association) 1 Article Cryptic diversity of Japanese Diaphanosoma (Crustacea: Cladocera) revealed by morphological and molecular assessments Csilla Lakatos,1,2 Jotaro Urabe,1 Wataru Makino1* 1 Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, Japan 2 Department of Ecology, University of Debrecen, Debrecen, Hungary * Corresponding author: [email protected] Received 13 March 2015; accepted 11 June 2015; published DD Month 2015 Abstract We found 5 distinct species of Diaphanosoma from a variety of lakes in Japan according to morphological examination and genetic analyses with the DNA sequences of mitochondrial 16S ribosomal RNA and cytochrome c oxidase subunit I genes (mtCOI). Previously, D. brachyurum was thought to occur at temperate regions including Japan; however, we did not find D. brachyurum in Japan. Instead, we found D. cf. amurensis, which inhabited mainly natural habitats of high altitude and latitude, and D. cf. dubium, D. cf. orientalis, and D. cf. macrophthalma, which occurred in a variety of habitats from large natural lakes to small artificial ponds at low altitude. We also found another species from only one pond that possessed mtCOI sequences that matched almost completely with those from North American specimens and thus was probably nonindigenous Diaphanosoma. Concordance between the results of morphological identifica- tions and genetic analyses showed that the DNA barcodes established in this study are useful to identify Diaphano- soma species in Japan and adjacent areas. Key words: Diaphanosoma, distribution, DNA barcode, mitochondrial cytochrome c oxydase subunit I (mtCOI) gene, mitochondrial 16S ribosomal RNA gene (mt16S) Introduction distributed cladocerans such as Holopedium gibberum (Rowe et al. 2007), Leptodora kindtii (Korovchinsky The genus Diaphanosoma is distributed world-wide, 2009, Xu et al. 2011), Chydorus sphaericus (Belyaeva except in Antarctica and New Zealand (Korovchinsky and Taylor 2009), and Polyphemus pediculus (Xu et al. 1992). In Japan, previous studies reported the occurrence 2009) has been rejected because each of these “species” of D. brachyurum in a variety of lakes and ponds, is assigned to more than one species. including pristine pools in high mountain moors (e.g., Recently, a thorough revision of Diaphanosoma based Taira 1989, 2000), large lakes of low altitude (e.g., on external morphology has restricted the occurrence of Kikuchi 1937, Murayama and Saisho 1967, Hanazato and D. brachyurum sensu stricto to the area from Europe to Yasuno 1987, Yoshida et al. 2001), and artificial Siberia and Central Asia (Korovchinsky 1992). Since reservoirs (Higuti 1960, Mizuno and Tetsukawa 1963, then, several Diaphanosoma species were recorded for the Watanabe 1965). This prevalence of D. brachyurum in first time in Japan, including D. dubium and D. orghidani Japan was largely due to using the European species (Korovchinsky 2000a, 2000b) and D. macrophthalma name under the belief that most zooplankton species are (Tanaka et al. 2004). In addition, 2 new species, D. cosmopolitan. After the 1970s, however, cladoceran orientalis (Korovchinsky 1986) and D. kizakiensis (Ko- taxonomy began to improve, with more detailed morpho- rovchinsky 2013), have been described based on logical descriptions and consideration of genetic data specimens collected in Japan. Korovchinsky (2013) has (Frey 1982, 1987, Korovchinsky 1997). As a result of also stated that Diaphanosoma amurensis is present and detailed studies, the cosmopolitanism in broadly D. excisum might be present in Japan. DOI: 10.5268/IW-5.3.847 Inland Waters (2015) 5, pp. © International Society of Limnology 2015 2 Lakatos C, Urabe J, Makino W. Although our understanding of the species diversity of S2) because these characters are useful for distinguishing Japanese Diaphanosoma has improved, as explained Diaphanosoma species recorded in Japan (Korovchinsky, above, little is known about ecological characteristics 1992, 2000b, 2013, Korovchinsky and Mirabdullaev such as the spatial distribution of these species within the 1995, Korovchinsky and Sheveleva, 2009). Note, Japanese islands. To clarify these ecological characteris- however, that for each of the above-mentioned Diaphano- tics, precise identification of Diaphanosoma at the species soma species, we did not examine specimens collected level is essential; however, the morphological diagnostic from the type localities outside of Japan (e.g., Uzbekistan characters of Diaphanosoma species are rather subtle and for D. macrophthalma). In the case of D. orientalis, unfor- minute, which may cause misunderstanding of the tunately, its type locality was not included in our sampling ecological characteristics of each species through misi- sites. In the present study, therefore, we appended a “cf.” dentification. In such situations, identification with the aid when naming Diaphanosoma specimens to avoid potential of DNA barcoding is known to be effective (Hebert et al. confusion with the naming of these species in the future. 2003, Costa et al. 2007, Rowe et al. 2007, Huemer et al. In genetic analyses, the 16S ribosomal RNA gene 2014). To date, however, there have been few genetic (mt16S) was sequenced for 2 individuals of each Diapha- analyses of Diaphanosoma species (Müller and Seitz nosoma species identified in each lake or pond. Their 1995, Elías-Gutiérrez et al. 2008, Briski et al. 2011, Young DNA was extracted with QuickExtract according to the et al. 2012, Prosser et al. 2013). manufacturer’s protocol. We then used the mt16S The objective of this study was to clarify the distribu- universal primers developed by Sarri et al. (2014) and suc- tion patterns of Diaphansoma species in Japan. Specifi- cessfully amplified a ~200 bp fragment for all individuals cally, we examined whether different Diaphansoma examined. The polymerase chain reaction (PCR) species occur in different types of lakes and ponds. For conditions consisted of 85 s of initial denaturation at 95 this purpose, we first morphologically identified Diapha- °C, followed by 35 cycles of 35 s at 95 °C, 1 min at 48 °C, nosoma collected in a variety of lakes and ponds across and 30 s at 72 °C, and a final extension of 5 min at 72 °C. Japan. Then, by developing a Diaphanosoma DNA After cleaning the PCR products with an ExoSap IT kit, sequence library, we examined the feasibility of morpho- we conducted cycle-sequencing with a BigDye Terminator logical identification of Diaphanosma species. We also sequencing kit. Sequencing was then executed from both checked whether any Diaphanosoma species should be directions with an ABI PRISM 3100-Avant Genetic treated as a complex of cryptic species. Finally, we used Analyzer (Applied Biosystems). Obtained sequences all the above data to compare the spatial distribution of (164–168 bp) were submitted to the DNA Data Bank of different Diaphanosoma species in Japan. Japan (DDBJ) under the Accession numbers LC059999 – LC060040. We edited the sequences with FINCH TV and Methods aligned them with CLUSTAL X (Thompson et al. 1997). The phylogeny of mt16S sequences was illustrated using a The present study used sets of ethanol-fixed Japanese neighbor-joining (NJ) tree, which was constructed in freshwater zooplankton samples (see Makino and Tanabe MEGA 6.06 (Tamura et al. 2013) applying Kimura 2 2009, Makino et al. 2010, 2013, Urabe et al. 2011 ) parameter (K2P) pairwise genetic distance, pairwise gap collected between 2003 and 2014. Samples from 316 deletions, and 1000 bootstrap replications. lakes and ponds collected between June and November in Because some studies have deposited partial sequences each year were examined. We found that Diaphanosoma of the mitochondrial cytochrome c oxidase subunit I was present in 137 of the 316 lakes and ponds; however, (mtCOI) gene of Diaphanosma in searchable genetic the condition of Diaphanosoma specimens was databases (Elías-Gutiérrez et al. 2008, Briski et al. 2011, suboptimal in 41 of these cases, and these were excluded Young et al. 2012, Prosser et al. 2013), we also examined from the analysis. Thus we analyzed Diaphanosoma the sequence of this gene region for several specimens individuals collected in 96 total lakes and ponds (see Sup- (Supplemental Table S1) to systematically compare plemental Table S1). Diaphanosma occurring in Japan with those in other We examined 2–4 adult females from each sampling regions. The mtCOI was amplified using a primer set of site by morphology. For the morphological identification LCO1490 and HCO2188 (Folmer et al. 1994) according of Diaphanosoma individuals, we inspected the head to the protocol in Makino and Tanabe (2009). The PCR shape, the relative length of the swimming antennae, the products were cleaned and sequenced as explained above, presence or absence of inner spines near the dorsal and obtained sequences (658 bp) were submitted to DDBJ junction of both valves of the carapace, and the patterns of under the Accession numbers LC060041–LC060059. We denticles and a thin setule along the posterior and postero- then aligned the obtained mtCOI sequences with those of ventral margins of the carapace (see Supplemental Table Diaphanosoma outside of Japan deposited in the genetic © International Society of Limnology 2015 DOI: 10.5268/IW-5.3.847 Cryptic diversity of Japanese Diaphanosoma 3 databases. The phylogeny of aligned sequences (529 bp) D. cf. dubium was divided
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